Wednesday, December 21, 2011

A Torley Defense of Irreducible Complexity

Vincent Joseph Torley (vjtorley) has a Ph.D. in Philosophy (2007) from the University of Melbourne (Australia). He currently teaches English in Japan.

Torley hangs out at Uncommon Descent where he tries to defend Intelligent Design Creationism. He didn't like my recent posting on Irreducible Complexity [Barry Arrington Explains Irreducible Complexity] because I accused Barry Arrington of not understanding evolution. You might recall that Arrington began his defense of irreducible complexity by saying, "(1) By definition, evolution can work only in a stepwise fashion wherein each successive step is “selected for” because it has conferred a selective advantage on the organism."

This is not how evolution is defined and it's a particularly bad way to begin because the scientific understanding of many irreducibly complex systems involves the fixation of neutral or even detrimental alleles. Competency in evolution also requires an understanding of redundancy, contingency, and sloppiness.

Let me state up-front that I am a philosopher, not a scientist. However, I believe in arguing rigorously, so I have attempted to state the argument from irreducible complexity in a rigorous fashion. I’d appreciate hearing from Professor Moran thinks of this argument, as a biologist.

Hmmm .... this seems like a pretty damning confession when your goal is to show that IDiots understand evolution well enough to know when it's impossible. I accused Barry Arrington of screwing up his defense of irreducible complexity because he started with an incorrect assumption about evolution. Now Torley weighs in with an up front confession that he, too, lacks expertise in the very subject he is criticizing. Doesn't anyone else find this a bit bizarre?

A functional system is irreducibly complex if it contains a multipart subsystem (i.e., a set of two or more interrelated parts) that cannot be simplified without destroying the system’s basic function. I refer to this multipart subsystem as the system’s irreducible core.

We can therefore define the core of a functionally integrated system as those parts that are indispensable to the system’s basic function: remove parts of the core, and you can’t recover the system’s basic function from the other remaining parts. To say that a core is irreducible is then to say that no other systems with substantially simpler cores can perform the system’s basic function.

It's important to keep this definition in mind because later on we'll see how Michael Behe changes the definition in light of biochemical facts.

Torely goes on to list several possible ways by which an irreducibly complex system could evolve by "unguided, Darwinian evolution." He then "proves" that none of them could work without ever discussing a single biological example.

I'm especially interested in his 4th example ...

(iv)(a) adds a new part to / alters an old part in an existing system with function G, thereby generating a system which is able to perform a brand new function F; {co-option} and/or {transformation}

...

Why (iv)(a) won’t work

However, it’s very unlikely that a system with function G, which gains one new part, while keeping the existing parts in nearly the same configuration as they were before, should suddenly be able to perform a totally new function F, especially if the number of parts in the system is large. Reason: the space of all possible configurations is astronomically large. However, the vast majority of configurations don’t do anything useful: they have no functionality. (Think of amino acid chains.) The number of possible functions is therefore much, much smaller than the number of possible configurations, and different functions are likely to be isolated on little islands of configuration space. If just adding one part to a complex system with an existing function G were enough to generate a system with a new function F, that would mean, contrary to supposition, that the two functions were relatively close together in configuration space. As the number of parts n of the complex system increases, however, this scenario becomes less and less plausible. (And now think of Behe’s bacterial flagellum. Even the simplest flagella require 30 parts. The idea that adding one part to an existing 29-part system would somehow magically confer the functionality of the flagellum appears to be extremely unlikely.)

But this is exactly how the irreducibly complex citric acid cycle arose! Most species of bacteria have a forked pathway for synthesis of organic acids. One of the forks, the oxidative pathway, leads to the synthesis of α-ketoglutarate from citrate and acetyl-CoA. α-Ketoglutarate is an important precursor for amino acid biosynthesis. The other pathway, the reductive pathway, leads to the synthesis of succinyl-CoA, a precursor of heme-like molecules. These species do not have a citric acid cycle.

Some bacteria have an additional enzyme, called α-ketoglutarate dehydrogenase, that converts α-ketoglutarate to succinyl-CoA thus forming a circular pathway by reversing the reductive pathway to create a way of oxidizing acetyl CoA and producing high energy molecules. Note that in the new circular pathway, a two-carbon molecule (acetyl group) is completely oxidized to two molecules of CO2 and the initial substrate (oxaloacetate) is regenerated. If you remove any of the enzymes in this pathway you break the circle and lose the ability to oxidize acetate.

The important points are that the citric acid cycle is an excellent example of an irreducibly complex system according to Dembski's definition and that it arose in a single step from two other pathways that had different functions.

THEME:Pyruvate
DehydrogenaseThe new enzyme, α-ketoglutarate dehydrogenase, carries out a very similar reaction to another important enzyme called pyruvate dehydrogenase and it's very clear that the new citric acid cycle enzyme evolved from pyruvate dehydrogenase [Pyruvate Dehydrogenase Evolution].

None of the other "proofs" that Torley offers are any better. It's quite easy to think of examples that correspond to the steps that Torley says are impossible.

Michael Behe is a biochemist. He knows about most of these examples and that's why his definition of irreducible complexity is tweaked in order to eliminate metabolic pathways like the citric acid cycle. Neither Torley nor Arrington (nor Dembski) are aware of these problems so they try to defend a version of irreducible complexity that Behe rejects. Here's what Behe says in Irreducible Complexity and the Evolutionary Literature: Response to Critics.

Finally [KEN LAM] Miller discusses a paper which works out a scheme for how the organic-chemical components of the tricarboxylic acid (TCA) cycle, a central metabolic pathway, may have arisen gradually. (Melendez-Hevia et al. 1996) There are several points to make about it. First, the paper deals with the chemical interconversion of organic molecules, not the enzymes of the pathway or their regulation. As an analogy, suppose someone described how petroleum is refined step by step, beginning with crude oil, passing through intermediate grades, and ending with, say, gasoline. He shows that the chemistry of the processes is smooth and continuous, yet says nothing about the actual machinery of the refinery or its regulation, nothing about valves or switches. Clearly that is inadequate to show refining of petroleum developed step by step. Analogously, someone who is seriously interested in showing that a metabolic pathway could evolve by Darwinian means has to deal with the enzymic machinery and its regulation.

The second and more important point is that, while the paper is very interesting, it doesn't address irreducible complexity. Either Miller hasn't read what I said in my book about metabolic pathways, or he is deliberately ignoring it. I clearly stated in Darwin's Black Box metabolic pathways are not irreducibly complex (Behe 1996) (pp. 141-142; 150-151), because components can be gradually added to a previous pathway. Thus metabolic pathways simply aren't in the same category as the blood clotting cascade or the bacterial flagellum. Although Miller somehow misses the distinction, other scientists do not. In a recent paper Thornhill and Ussery write that something they call serial-direct-Darwinian-evolution "cannot generate irreducibly complex structures." But they think it may be able to generate a reducible structure, "such as the TCA cycle (Behe, 1996 a, b)." (Thornhill and Ussery 2000) In other words Thornhill and Ussery acknowledge the TCA cycle is not irreducibly complex, as I wrote in my book. Miller seems unable or unwilling to grasp that point.

Let me clarify Behe's point. The citric acid cycle is irreducibly complex by most of the definitions offered by Intelligent Design Creationists. However, Michael Behe—the only biochemist on the team—says that pathways like the citric acid cycle can't be irreducibly complex because it's too easy to see how they could evolve in a stepwise manner.

I wish the IDiots would get their acts together because it would be a lot easier to refute them all at once instead of having to deal with several different versions of each attack on evolution. Let me help out by giving them the latest version of irreducible complexity that takes real science into account.

An irreducibly complex system is a complex system where every part is needed for its function. An irreducibly complex system cannot be produced by any known evolutionary mechanism because as soon as such an explanation becomes available the complex is, by definition, no longer irreducibly complex.

In comment 10 of http://whyevolutionistrue.wordpress.com/2011/12/20/did-darwin-plagiarize-wallace/, “Ant Allan” remarked:Isn’t it a rule of thumb that if any science-related article is entitled with a question, the answer is always, “no”?

How many components does the citric acid cycle contain? Behe's mousetrap contains 5.

Next what is the evidence that A) the first two pathways arose via ccumulated random mutations and B)the new/ additional pathway arose via random mutation(s)?

The point being is that ID challenges the premise that all mutations are random/ accidents/ mistakes. And the number of components is explained by Behe- to wit you cannot refute all of IC by demonstrating that a simple, ie 1-3 parts, system can arise via stochastic processes.

"How about Professor Coyne’s concern that, if one system were shown to be the result of natural selection, proponents of ID could just claim that some other system was designed? I think the objection has little force. If natural selection were shown to be capable of producing a system of a certain degree of complexity, then the assumption would be that it could produce any other system of an equal or lesser degree of complexity. If Coyne demonstrated that the flagellum (which requires approximately forty gene products) could be produced by selection, I would be rather foolish to then assert that the blood clotting system (which consists of about twenty proteins) required intelligent design."

What "mainstream scientists", like Kenneth Miller, don't seem to understand is that all systems of function are irreducibly complex regardless of whether or not a working subsystem can be found within the larger system.

It would be just lovely if people who admittedly lack the fundamental education to comment on a complex subject would leave it to the experts. Of course, since ID is a fraud, I suppose anyone can be an expert by declaration, as with homeopathy and fortune telling.

In a comment at your previous post I explained why metabolic pathways are not IC. Apparently you missed it. So I'll simply copy and paste it here. Perhaps this time you will read it:

If I understand it, metabolic systems are systems where enzymes interact with substrates (I hope that's the correct term) instead of with each other. Thus Enzyme A interacts with substrate A, which is transformed into substrate B, which allows Enzyme B to interact with it, etc. Behe points out in his book that it is possible for such a system to evolve gradually, starting with what is now the last substrate (e.g., substrate D) and working backwards to what is now the first substrate (e.g., substrate A). Thus, it is possible for such a system to evolve one protein at a time, while still producing the same final end product.

Contrast this with an IC system, where each protein interacts with other proteins, where removing one of them causes the entire system to cease functioning. Now it might still be possible that the remaining proteins might still interact with each other to achieve a different function. And that might be one way of showing that they in fact evolved indirectly.

So other than the citric acid cycle, which is a metabolic pathway, not an IC system, do you have any other examples of how an IC system evolved?

"The point being is that ID challenges the premise that all mutations are random/ accidents/ mistakes."

And :

"BTW stop blaming us because you cannot or refuse to understand IC."

Joe, you regularly say that you IDiots must first show that the ToE is wrong before you can even posit ID. Well, the way you can show that the ToE (or parts of it like random mutations) is wrong is by showing what alternative is right.

"If natural selection were shown to be capable of producing a system of a certain degree of complexity, then the assumption would be that it could produce any other system of an equal or lesser degree of complexity."

joe, have you heard the term "eco-system"? How would you define "eco-system", how many parts are there in an eco-system, is an eco-system "complex", and can the term "stochastic" be applied to any eco-system?

"Those who are familiar with the work of Dr. Douglas Axe will recognize the problem I’m talking about. Only a tiny fraction of amino acid sequences are in any way functional. The odds against proteins such as citrate synthase forming in this way are astronomical."

Which seems to say that there may be a greater proportion of amino acid sequences that are functional than VJT supposes.

For another example, simply look at the capsid proteins of norovirus. There is extensive variation, but each variant does the same job. There are also reports of polymerases in which the amino acids of the active site itself can be extensively substituted whilst the enzyme retains function

Umm there isn't any relevant work on the evolution of the flagellum via an accumulation of random mutations.

YOU cannot even produce a testable hypothesis for the claim.

You do realize that there is a huge difference between identifying similar proteins and then getting the proteins in the right place, the right time and in the correct correct quantities- never mind getting them into the proper configuration, which requires chaperones to avoid cross-reactions.

So have at it Nick, Larry or any other evo- produce a testable hypothesis for the alleged evolution of the bacterial flagellum via accumulations of random mutations.

I love what we learn about the Designer (capital D) in the UD post. Did you know that the Designer either (i) is made of one chunk (no parts!) or (ii) has parts that are inseparable from one another (glued together?) or (iii) is reducibly complex (maybe He/She/It evolved from a simple predecessor?). You never hear theologists about THAT kind of stuff.

OK guys, here a warning. While Joe G might show some capacity of thinking when using some arguments, when answered he seems to shutdown his understanding systems. So much so that even if you showed clearly that he does not understand evolution one bit, he would still repeat that you have not answered time and again. Consider yourselves warned.

Those of us who follow the Joe G traveling circus as he trolls various C/E boards like to play “Joe G Bingo”. Joe never makes coherent arguments but has a collection of inane one-liners he uses for every occasion, i.e.

“Nature operating freely”“ID isn’t anti-evolution”“Design is a mechanism”“Your position has no evidence”“Your position has no testable hypotheses”“Your ignorance isn’t a refutation of ID”“Cause and effect proves ID”“blind, undirected chemical processes can’t construct multi-part systems.”“Earth is a privileged planet”“Blind watchmaker processes”“The evidence supports baraminology”

"Correcting Four Misconceptions about my 2004 Article in JMB" (May 4, 2011). Sounds like he now regards the evolution of protein folds as the result of an unguided process as astronomically improbable.

The basic idea behind cladistics is that members of a group share a common evolutionary history, and are "closely related," more so to members of the same group than to other organisms. These groups are recognized by sharing unique features which were not present in distant ancestors. These shared derived characteristics are called synapomorphies.

By your question I am starting to think that you don't know what "testable hypothesis" means.

Also, you seemed to contradict that notion that the parts forming your proposed (and long-time quite explained) IC system the flagellum are so finely made to fit each other. If they are, why do you need chaperons to avoid cross-reactions? Could it be that those proteins might fit somewhere else besides their place in the flagellum? Could that indicate that "fitting" is not that hard to evolve?

Then also, do you think the flagellum is assembled by a little intelligent designer every time one is produced? I ask because your questioning implies that you are thinking assemblage (putting the pieces in the right place, correct concentrations ...), rather than evolution.

Just curious. I know how useless it is to explain anything to you, so I rather let you illuminate us with your wisdom.

Gee Negative Entropy, to correct me all you have to do is produce a "valid" testable hypothesis for your position. Then we could all see what a "real" testable hypothesis for a "real" scientific position looks like.

Now you blather on as if the falgellum has been long-explained. Well it hasn't been explained via scientific data.

Also your position can't explain chaperones beyond "look at those there thingies"

BTW as I have said there isn't any need for a designer to assemble- all that is required is a genetic algorithm to make it so. And ID is NOT anti-evolution. You are still confused.

As far as explaining things to me- no I am not a gullible fool and I require scientific evidence, not your bullshit, for explanatory power.

Nice to see all you can do is throw out false accusations- truly pathetic...

I never said that. I say the design inference is based on our KNOWLEDGE of cause and effect relationships. I take it that since you don’t understand what “knowledge” is you were confused by the whole thing.

VJT, whatever Axe saidm about his 2004 paper, I cited his 1996 paper, in which he showed that he could pretty well randomise the hydrophobic core of an enzyme and still retain its function.And of course you have not addressed the fact that many many proteins can be extensively mutated, truncated, and otherwise fiddled with and still retain functionIt may well be true that SOME proteins are exquisitely sensitive to sequence changes, but by no means is this true of all proteins - my suspicion is that it is true of only a minority of such.

I myself routinely use luciferases that have been mutated in various ways to tailor their properties for particular purposes. They are all still identifiably and incontrovertibly luciferases, despite multiple sequence alterations.

TWiT:joe, have you heard the term "eco-system"? How would you define "eco-system", how many parts are there in an eco-system, is an eco-system "complex", and can the term "stochastic" be applied to any eco-system?

Make your point- or rather erect your strawman and show how it apples to anything without resorting tio question-begging.

Thorton. You might as well add this to Joe's one liners. "You have not answered anything" and derivatives.

Joe has another one-liner he's been leaning on heavily of late: "evolution is an intelligently designed genetic algorithm!"

Other than that, it's the same ol' same ol' from Joe-boi. The inane blithering, the insults and obscenities, the evasion of questions, the PRATT regurgitation of IDC claims. He has been careless in letting his YEC beliefs show again however, arguing for a literal Noah's Ark here.

Joe is mentally ill similarly to the David Mabus / Dennis Markuze C/E stalker, except Joe always craps his pants and flees when his bluff is called.

JoeG asks "Where is your testable hypothesis?" As one example, Wagner and Chiu, http://tinyurl.com/852rhcy, offer a multi-part hypothesis for the evolution of limbs from fins.

Hypothesis testing is possible only if you understand the underlying causality. But ID has no causes on offer, which means that it can't generate hypotheses. Indeed it has no explanatory power at all. "God did it" is an explanation only if you understand some causal details of how God works.

"Well, the way you can show that the ToE (or parts of it like random mutations) is wrong is by showing what alternative is right."

joe g said:

"I disagree. By showing that I can design someting does not rule out that it could have happened by accident.

If I go imnto a lab and design a ribosome it does not refute the ToE."

joe, I don't recall saying anything about you designing something, or anything about an accident.

You constantly say that a "designer" is responsible for the diversity of living things (evolution). You constantly say that there's no evidence for what you call "blind watchmaker" (not designed) evolution. You also constantly say that scientists don't even have a testable hypothesis for "blind watchmaker" (not designed) evolution. And, you constantly say that the way to prove ID wrong is to prove "blind watchmaker" (not designed) evolution right.

So, going by your own stated standard for how a theory, hypothesis, or inference (take your pick) can and should be proven to be wrong, you IDiots must have evidence and a testable hypothesis and you must prove that your "alternative" hypothesis is right.

If you want to modify or replace a theory, hypothesis, or inference of naturalistic evolution, you must at least have evidence and a testable hypothesis for your alternative. You IDiots can't even show that you have any potentially testable evidence or a potentially testable hypothesis. Everything you IDiots assert is based on your religious beliefs, which are based on an imaginary, miracle-performing, supernatural god and the fairy tales associated with that god.

Whether you can design something or not is irrelevant. What matters is whether you can show, with testable evidence and a testable hypothesis, that your imaginary designer god is responsible for the diversity of living things.

Now, you'll probably say that scientists haven't proven that strictly natural causes are responsible for the diversity of living things, but of course there are a few things that you never understand or accept. There's no reason for science to consider anything but natural causes, there's no way for science to investigate supernatural causes (like imaginary gods or pink unicorns), and science is actually working on finding all the causes, which is a lot more than can be said about "your position".

Your "position" (i.e. you IDiots) just sit around and bash anything and anyone that doesn't conform to your asinine beliefs. You don't do any actual scientific investigation, research, studies, tests, etc., and you haven't proposed any scientifically testable evidence or a testable inference, hypothesis, or theory that would support your claims of a designer (your chosen god). Your 'beliefs' aren't enough.

By the way, joe, can you please calculate the amount of "CSI" in a banana and show your work? If you don't have a banana handy, how about a watermelon or a tick?

You also said:

"I am not a gullible fool and I require scientific evidence"

And your "scientific evidence" for the existence of your chosen designer god is...?

And which one is your chosen designer god, yhwh or allah? You seem to bounce back and forth between the two.

"joe, have you heard the term "eco-system"? How would you define "eco-system", how many parts are there in an eco-system, is an eco-system "complex", and can the term "stochastic" be applied to any eco-system?"

And got a non-answer from joe. So, I'll try to explain why I asked him those questions and I'll try to make it simple enough for him to understand.

Okay, joe, picture this:

A new volcanic island appears in an ocean. At first the island is barren of life. Gradually the island is modified by weather, and streams and ponds form. While this is happening or after it happens some living things make it to the island. Some of those living things survive and populate the island, or at least parts of it. Plants grow on the land and in the ponds and streams, aquatic creatures live in the ponds and streams, flying insects and birds fly around, molds, fungi, and lichens appear, even some reptiles and amphibians show up. Maybe even a rodent or three. A many-part 'complex' eco-system forms, and of course that eco-system is subject to change (including extinction).

As I said, some things survive, while others do not. Some things are food for other things. Weather and other factors also affect the survivability of whatever living things happen to get there.

Many more living things make it to the island than will survive and thrive there and of course not all of the individuals of the species that do survive and thrive there will survive and thrive.

Nature will 'select' what survives and thrives and what doesn't. Stochastic (non-deterministic) causes and/or process are responsible for the plants and animals that get there in the first place and are also responsible for what survives and thrives there.

Do I also need to get into the changes (evolution) that will eventually occur in the surviving resident species?

Now, you're likely wondering what any of that has to do with 'systems', selection, or stochastic processes/causes at the molecular or genetic level. I'd say it's a matter of scale. Factors (at least some of them) that apply to the inhabitants of the island also apply at a smaller scale. After all, everything on the island, and even the island itself, is a 'complex' assemblage of very tiny parts. The entire eco-system of the island is a 'complex' assemblage of 'parts', some being symbiotic and others competitive. Some, if not all parts could also be described as "irreducible"

So, do you think that the island eco-system I described would have to be intelligently designed or can an eco-system form without an intentional plan or goal?

But "Honda did it" is a perfectly good explanation of my car. I can even test this as a hypothesis. Or ET did it, I think we are searching for such signals in space.

In fact, Sal Cordova had a hypothesis he called "DNA steganography," where he proposed that somewhere in the genome is hidden an actual coded message along the lines of "God did this." (Why it should be hidden I don't know. The Bible does not seem to indicate God was shy in the past about showing His handiwork - pillars of fire, seas splitting, etc., etc.)

lee, you be sure and let us know the instant that the many high-dollar ID research programs analogous to SETI (which I'm sure must be legion) find that message, OK?

- Why should the designer exempt metabolic pathways, which are of course critical to survival?

- What is the fundamental biochemical difference between metabolic pathways and, e.g., the blood clotting pathway that enables the former type of pathways to evolve, but absolutely prohibits this from happening in the latter (except for lobsters, of course, but they're not relevant because, well, er, because, umm...)?

An ecosystem is not irreducibly complex. A damaged ecosystem still "works" - sort of. In any case, some organisms in an ecosystem are of more ecological significance than others - keystone species in particular.

("The Teleological Argument: An Exploration of the Fine-Tuning of the Universe" by Robin Collins. In The Blackwell Companion to Natural Theology. Edited by William Lane Craig and J. P. Moreland. 2009. Blackwell Publishing Ltd. ISBN: 978-1-405-17657-6.)

Believe it or not, I'm working on your CSI-in-a-banana question. I've been digging and delving for a few months, on and off. If you want to help, see if you can dig up the following:

What's the compressed size of an E. coli genome? (using UCSC genome browser database figures, which I seem to have trouble accessing)

The statements "Only a tiny fraction of amino acid sequences are functional" and "Proteins can remain functional even when a large number of changes are made" are mathematically compatible. To see why, have a look at Axe's 2010 paper, "The Case Against a Darwinian Origin of Protein Folds", BIO-Complexity 2010(1):1-12. doi:10.5048/BIO-C.2010.1. See especially pages 5-6. Web address:

"An ecosystem is not irreducibly complex. A damaged ecosystem still "works" - sort of. In any case, some organisms in an ecosystem are of more ecological significance than others - keystone species in particular."

The definition you rely on for a "system" says:

"A functional system is irreducibly complex if it contains a multipart subsystem (i.e., a set of two or more interrelated parts) that cannot be simplified without destroying the system’s basic function. I refer to this multipart subsystem as the system’s irreducible core.

We can therefore define the core of a functionally integrated system as those parts that are indispensable to the system’s basic function: remove parts of the core, and you can’t recover the system’s basic function from the other remaining parts. To say that a core is irreducible is then to say that no other systems with substantially simpler cores can perform the system’s basic function."

And you said this in a post on UD:

"Recall the definition of irreducible complexity: “a set of two or more interrelated parts that cannot be simplified without destroying the system’s basic function.”"

Organisms aren't the only parts of an eco-system. I was being very general in my previous description of the island eco-system but you might notice that I mentioned the island itself and weather. I also mentioned "other factors". I figured that I shouldn't have to spell out every specific thing ("part") that would affect (or destroy) the "function" of the eco-system. I guess I was mistaken.

However, I'm still going to be very general (for now at least) and just propose a couple of basic things, with systems, sub-systems, and "core" in mind:

1. Remove the fresh water from the eco-system.

Or,

2. Remove the island (the land itself).

Would the island eco-system still "function"?

I read the Collins article. To me it's just a lot of sciency sounding words that try real hard to justify belief in an imaginary god and the belief that humans are the pinnacle of special creation in a universe that was specially created and fine tuned for humans by that alleged god. It's a massive demonstration of typical godbot arrogance.

It's also interesting (and amusing) that you would offer that article as "scientific evidence" even though it's overflowing with non-scientific assertions and proselytizing. And, in the article Collins says this:

"But what about the scientific strictures of methodological naturalism? These would be relevant only if the appeal to God were considered as a scientific explanation, something that I am not assuming. Rather, God should be considered a philosophical or metaphysical explanation of LPU." (life-permitting universe)

Apparently, Collins doesn't think that his argument is scientific.

By the way, could a "damaged" flagellum still work - sort of?

And just out of curiosity, do you think that humans are "indispensable" and that if all humans were removed that the "core" eco-system(s) or just plain old system(s) of the Earth and/or the universe would cease to "function"?

Back to irreducible complexity. I have a simple question. My irreducible complexity argument hinges on the background assumptions that:

(i) functions possessed by newly added components in isolation seldom carry over into the larger unit that they become part of; and

(ii) biological functions are highly configuration-sensitive. In other words, if you've got two parts - let's call them A and B - where A is a chain that is already made up of lots of smaller parts that have been previously added, and then B gets added to A, then I would expect that:

(a) whatever function B may have had in isolation, it probably won't continue to work that way after it is joined to A;

(b) a new function of B might emerge after it has been joined to A, but it would only emerge if it was joined to A in just the right way. In other words, it would be very configuration-sensitive. What's more, if B were configured to A in the wrong way, that might damage or destroy A's existing functionality.

Given my assumptions, I hope you can see why the successive build-up of functions by adding bits B, C, D, ... to A appears extremely unlikely. But if assumptions (i) or (ii) are mistaken, then my argument would collapse.

You're a biochemist; I'm not. Is there something I'm missing here? Which, if any, of my assumptions is mistaken?

Intelligent designers have more methods at their disposal than attempting random combinations of elements and hoping for function. That’s an especially useless plan if you’re looking for a specific function.

An intelligent designer imagines screws that are inserted with screwdrivers. He does not arrange random configurations of metal and suddenly say, “Look! This four-pronged configuration is useful for both impaling food and twirling noodles. I wasn’t looking for that, but having stumbled upon it, how convenient. I can’t wait until another random configuration of elements and processes produces noodles.” And then, millions of attempts later, after attempting all sorts of random additional ingredients such as mustard, sand, and horse excrement and finding them less than desirable, the designer stumbles upon a paste made from boiled tomatoes which incrementally improves on the unadorned noodles. At last!

Can you see how useless such an approach would be for designing something as simple as screws and screwdrivers, which have no purpose whatsoever except as part of a separately envisioned design?

You assert, against all evidence and common sense, that designers must act by random variation and selection, and then place the burden on others to explain how that might work.

Intelligence is not so limited. I think this has been said over and over – that’s what makes it “intelligent.”

I provided the above example to help illustrate something that really bugs me about the arguments for intelligently designed IC, complex specified (functional) organized information, fine tuning, and ID in general. I've asked IDiots questions similar to the following ones several times but have never gotten an answer.

So, I'll try asking here and give the IDiots a chance to respond.

So, if the alleged intelligent designer is so intelligent and so skilled and so knowledgeable and has so many resources at its disposable that it can design and create a universe and everything in it, including complex life forms with designed irreducible parts and systems and all the other stuff that the IDiots claim is present and necessary for "function" of those life forms, then WHY are there 'flaws' in those life forms? In other words, WHY are life forms often born with (or later acquire) disabilities, diseases, disfigurement, problems with function, and/or other 'flaws', and WHY do those life forms age and die (stop functioning), and why are many organisms born dead?

I can hardly wait for some IDiot to say that it's because of "the fall", since they claim that ID is scientific, not religious.

IDiots are real quick to argue that all the allegedly intelligently designed, irreducibly complex, specified, functional, digital, organized, blah blah, blah, etc., fine tuned stuff in living things and most or all other things is evidence or even proof of their chosen god (aka intelligent designer), BUT when it comes to flaws, the IDiots ignore the fact that the alleged designer (aka god) would be responsible for all of them too. And since "God" (aka intelligent designer) is alleged to be perfect, omnipotent, and omniscient, how can the IDiots explain the flaws?

Godbots always give their imaginary god credit for what they consider the good stuff but never for the bad (or flawed) stuff. To them, the bad stuff is the fault of man, or at least the first two people, even when the bad stuff happens to things other than man. What they conveniently forget is the story about "in his image". Obviously, based on "empirical observation" (a favorite term among IDiots) "God's" image is flawed.

"One question may possibly have dwelt in the reader's mind during the perusal of these observations, namely, Why should not the Deity have given to the animal the faculty of vision at once? Why this circuitous perception; the ministry of so many means; an element provided for the purpose; reflected from opaque substances, refracted through transparent ones; and both according to precise laws; then, a complex organ, an intricate and artificial apparatus, in order, by the operation of this element, and in conformity with the restrictions of these laws, to produce an image upon a membrane communicating with the brain? Wherefore all this? Why make the difficulty in order to surmount it? If to perceive objects by some other mode than that of touch, or objects which lay out of the reach of that sense, were the thing proposed; could not a simple volition of the Creator have communicated the capacity? Why resort to contrivance, where power is omnipotent? Contrivance, by its very definition and nature, is the refuge of imperfection. To have recourse to expedients, implies difficulty, impediment, restraint, defect of power. This question belongs to the other senses, as well as to sight; to the general functions of animal life, as nutrition, secretion, respiration; to the economy of vegetables; and indeed to almost all the operations of nature. The question, therefore, is of very wide extent; and amongst other answers which may be given to it; beside reasons of which probably we are ignorant, one answer is this: It is only by the display of contrivance, that the existence, the agency, the wisdom of the Deity, could be testified to his rational creatures."From pages 38-40 ofWilliam Paley, Natural Theology; or Evidences of the Existence and Attributes of the Deity, Collected from the Appearance of Nature (12th edition)taken from the online "The Complete Works of Charles Darwin Online"http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=A142&keywords=contrivance&pageseq=45

I don't know how Paley knew that limitation on the power of God, that God could only achieve his goals by the display of contrivance. Why could not the existence, the agency, the wisdom of the Deity be testified without contrivance? And why, in the 200 years since Paley, has no one answered this rather obvious question?

If you want a scientific answer to the question of why there are flaws in living things if they are designed, then I'd be happy to give you one.

(1) If living things were flawless then they'd never mutate and never evolve.

(2) You might ask why a Designer wouldn't just make each species separately. Short answer: too much work.

(3) Let's assume that the Designer works according to some sort of "Least Action" principle: He accomplishes His desired effects in the simplest way possible.

(4) Let's assume that the Designer's desired effects are: the production of intelligent and sentient life-forms, together with whatever other life-forms they require to support their way of life, in a world that requires as little external (Deus ex machina) intervention as possible.

(5) The simplest way to accomplish those effects would be to produce a primitive cell, endow it with a mechanism for evolving and diversifying into various life-forms, and then (at a few critical junctures) guide its evolution towards the desired targets. That would require some manipulations on the Designer's part, but relatively few. It would be much less work than specifying and creating each species.

(6) If the Designer's interventions are limited to guiding evolution at the odd juncture every few million years or so, and if the Designer works according to a "Least Action" principle, then obviously you wouldn't expect him to continually intervene in order to protect individual living creatures from deleterious mutations. And according to the foregoing picture, we don't know that the Designer cares about individuals anyway.

(7) You might wonder why the Designer couldn't make a primitive cell that could evolve into human beings without any guidance. Short answer: because that's impossible, even for an omnipotent Designer. More accurate answer: perhaps He could do such a thing, but it would require a LOT more work (in terms of detailed specifications) in order to set up initial conditions and laws that were guaranteed to produce a human being after four billion years (think: billiard ball collisions). Since the Designer works according to a Least Action principle, it would actually be easier for Him to make a cell and nudge its evolution from time to time.

(8) ID theory doesn't claim the Designer cares about individual creatures. If the Designer's goal is simply to produce intelligent and sentient beings, then that should suffice to answer your question.

(9) During the long process of evolution, all lineages (including our own) would pick up their share of bad mutations and junk DNA. The Designer wouldn't be concerned about that, as long as it didn't interfere with His prime objective of producing intelligent and sentient beings. My guess is that He's just let the junk accumulate, if He worked according to a Least Action Principle.

(10) If you really wanted to undermine ID theory, you'd have to show that the FIRST living cell must have contained genetic flaws that no competent Designer would have put there, AND that the subsequent evolution of intelligent and sentient animals could still have proceeded if these genetic flaws had been removed. Now THAT would create problems for ID.

sez vjtorley: "You might ask why a Designer wouldn't just make each species separately. Short answer: too much work."When ID's critics talk about what characteristics the Designer might have, IDiots often say gosh, we can't say anything about the Designer! all we're interested in is the Design -- questions about the Designer, such as what Its motives might have been or what tools It used, are theological questions, and therefore quite outside the scope of proper ID science. On what grounds, then, do you, vjtorley, assert that "too much work" is a factor the Designer would even notice, let alone form Its work habits around?

"Let's assume that the Designer works according to some sort of 'Least Action" principle: He accomplishes His desired effects in the simplest way possible."Why should we assume that? If we're just observing Nature and seeing what conclusions may be drawn from those observations, it's patently obvious that living things are bloody complicated things. If the Designer is indeed interested in using simple ways to accomplish Its goals, what's up with all the complexity of Life? Why, if the Designer prefers simple effects, are living things anything but simple? If a simplicity-preferring Designer produced living things to achieve some goal or other, wouldn't Designer-made living things have been, well, simpler than the fantastically jury-rigged Rube Goldberg 'mechanisms' that we know them to be?And of course, there's also the question of how the heck an IDiot can justify making any claims whatsoever, about the Designer's preferences as regards simplicity vis a vis complexity, given that ID explicitly denies it can have anything to say about any details regarding the Designer, said preferences being just one of those details...

If you want a scientific answer to the question of why there are flaws in living things if they are designed, then I'd be happy to give you one.

Not sure how what followed was a scientific answer, rather than idle speculation, but ...

(1) If living things were flawless then they'd never mutate and never evolve.

Very, very few of the mutational 'flaws' possessed by individual organisms are of evolutionary importance. Most lead to elimination from the gene pool. Evolution could proceed, in 'perfect' organisms, by novel, directed mutation.

(2) You might ask why a Designer wouldn't just make each species separately. Short answer: too much work.

The Idle Designer Hypothesis? You want to take that one up with the YECs.

[snip]

(9) During the long process of evolution, all lineages (including our own) would pick up their share of bad mutations and junk DNA. The Designer wouldn't be concerned about that, as long as it didn't interfere with His prime objective of producing intelligent and sentient beings. My guess...

It would be near-impossible to have such a goal without 'bad mutations' interfering with it. Any mutation can have an evolutionary impact, and influence the outcome of this chaotic, stochastic process. Random mutation demands constant tinkering.

(10) If you really wanted to undermine ID theory, you'd have to show that the FIRST living cell must have contained genetic flaws that no competent Designer would have put there, AND that the subsequent evolution of intelligent and sentient animals could still have proceeded if these genetic flaws had been removed.

Translation: "I'm just going to stick the goalposts out here on Pluto.".

Two points:

a) it is unlikely that there was a 'first cell', in the sense of an organism that we would describe as truly cellular and which had no parent, or whose parent was non-cellular. Cells-as-we-know-em arose gradually, from simpler replicators. Regardless, their 'flaws' such as we might understand the term, and the expectation of what a competent designer might do, must be judged in the context of their environment and ecology, to which we are not privy.

b) We'd have to demonstrate that we could go back 3.5 billion years and make a change to a nucleic acid strand, without changing the end result of the stochastic processes flowing from that strand? Jeez, you don't want much. Yep, I guess ID theory is really unassailable, then.

Thank you for your post. "Motive" and "goal" are two different concepts. I imputed a fairly broad goal to the Designer: the production of intelligent and sentient beings. I would argue that the fine-tuning argument (which ID proponents often appeal to) lends support to this claim. But I would not wish to speculate as to the Designer's motives.

It is a hallmark of intelligent beings that they tend to achieve their goals in the most efficient manner possible. Hence my "Least Action" principle. I don't see anything remotely theological about it. I also don't believe in radical agnosticism about the Designer of life and the cosmos - and if some ID proponents do, then all I can say is: good luck to them. All scientific working hypotheses need to start somewhere. My starting assumption is that the Designer planned to produce intelligent and sentient beings in the most concise possible way, where "concise" refers to the length of the total description of the initial conditions, laws and any external manipulations used to achieve the goal intended. What I'm assuming, in other words, is that the Designer's M.O. is the one with the lowest Kolmogorov complexity.

Finally, you ask why life couldn't be simple. I would answer that life is as simple as it can be, given the range of functions it has to carry out. Of course, you are perfectly free to prove me wrong. If you can design a radically simpler cell than the ones we find in Nature, with the same biological functions and capacity to evolve, then please do.

Finally, I don't care what you call me, but I do think it's rude to dismiss scientists of the caliber of Michael Behe and Douglas Axe, who have both published in PNAS, as "IDiots".

" Sounds like he [Axe] now regards the evolution of protein folds as the result of an unguided process as astronomically improbable."

Good for him. With the spectacular success of the Biologic Institute and its own top-notch, upper-tier journal whose every issue is jam-packed with irrefutable pro-ID science, no doubt that Axe will soon be a household name upon winning the Nobel. Perhaps he and the Biologic Institute's homemaker-turned ID scientist will soon grace the OWN channel.

"It may well be true that SOME proteins are exquisitely sensitive to sequence changes, but by no means is this true of all proteins - my suspicion is that it is true of only a minority of such.

IDCs are like that - they come across one paper documenting a single functional bit of non-coding DNA, for example, and we find a half-dozen "papers" on creationist websites declaring the death of 'darwinism' because all junkDNA has been proven functional...

I don't believe in setting goalposts on Pluto. In a recent post, Professor Moran argues that our genome is full of junk DNA. See here: http://sandwalk.blogspot.com/2011/10/stephen-meyer-talks-about-junk-dna.html

My question is a simple one: how far back can we trace the flaws in our genome? If they go back to the very beginning of life, then that would be a problem for ID.

sez vjtorley: "Thank you for your post. 'Motive' and 'goal' are two different concepts."That's nice. It doesn't alter the fact that bog-standard IDism explicitly asserts that we puny humans can't say nothin' about the Designer, and explicitly denies that it (ID) has any interest whatsoever in attempting to learn anything about the Designer, but it's nice.

"I imputed a fairly broad goal to the Designer: the production of intelligent and sentient beings."Yes, you did impute that goal to the Designer. Why did you, an ID-pusher, do that? If you were a real scientist performing actual research into Design, imputing some Goal X to the Designer would be fine, as long as there were some way of testing the hypothesis that the Designer actually did want to achieve Goal X; but you are an ID-pusher, not a real scientist. And ID (to repeat, because your failure to make note of it the first time suggests that repetition is in order) explicitly asserts that we puny humans can't say nothin' about the Designer, and explicitly denies that it (ID) has any interest whatsoever in attempting to learn anything about the Designer.

"I would argue that the fine-tuning argument (which ID proponents often appeal to) lends support to this claim. But I would not wish to speculate as to the Designer's motives."Your goal-vs-motive schtick is a distinction without a difference. If ID realio, trulio doesn't address any questions about the Designer, you ID-pushers have no grounds whatsoever on which to attribute either 'goal' or 'motive' to your Designer! At least, no grounds within the scientific framework of ID... which, like, is an honest-to-Francis-Bacon SCIENTIFIC FRAMEWORK™. Right?

sez vjtorley: "It is a hallmark of intelligent beings that they tend to achieve their goals in the most efficient manner possible."Of course, what is or isn't 'possible' for any given intelligent being, depends in large part on what constraints that may happen to be working under. And since ID explicitly asserts that we puny humans can't say nothin' about the Designer, and explicitly denies that it (ID) has any interest whatsoever in attempting to learn anything about the Designer, I really don't see how ID even can tell us anything about what constraints the Designer may or may not have been working under.

"Hence my "Least Action" principle. I don't see anything remotely theological about it."Groovy. Now clue in your IDiot buddies -- you know, the ones who've been making noise about how 'what are the Designer's goals?' is a theological question, hence not amenable to scientific study.

"Finally, you ask why life couldn't be simple. I would answer that life is as simple as it can be, given the range of functions it has to carry out."And I would argue that your answer is bullshit. However 'complex' the human body is, surely leaving out a part would make it less 'complex' than it is -- so wherefore the plantaris tendon? Something like 1/3 of all humans don't have it at all, and in the humans who do have a plantaris tendon, the damn thing is only connected on one end! What 'function' can the Designer possibly have had in mind for humans to fulfill, which requires a singly-connected tendon?

"Finally, I don't care what you call me, but I do think it's rude to dismiss scientists of the caliber of Michael Behe and Douglas Axe, who have both published in PNAS, as 'IDiots'."Right, because calling someone an 'IDiot' is so much worse than holding them responsible for most of the world's evils, up to and including the Holocaust. And if you're honest, vjtorley, you know very well that your fellow IDiots damn well have slandered real scientists by blaming them for most of the world's evils, up to and including the Holocaust. So how about you just take those pearls you're clutching, and shove 'em up the bodily orifice of your choice, hm?With regard to Behe: This man is on record -- he swore under oath and everything -- as asserting that science should be redefined to include ID, and that under his preferred science-redefinition, astrology is as good a science as ID! Behe has also put forth an 'evolution can't generate IC structures' argument which ignores the fact that evolutionary step-changes can include modification and/or removal of a structure's existing parts. Given these gross failures of his intellect, I'll call him an IDiot if I damn well feel like it, thanks very much for asking.

But you already have with your invocation of "too much work" re separate design of each species. Why design the huge numbers of ancient and current species then?

It is a hallmark of intelligent beings that they tend to achieve their goals in the most efficient manner possible. Hence my "Least Action" principle.

This is a statement of such scope, generality and vagueness as to rival horoscopes. If there is indeed a generalizable hallmark of intelligent beings regarding efficiency, it iwould seem to be that they tend to spend a great deal more time in apparently aimless play than less intelligent beings. Please consider for example the development of bees vs. that of chimpanzees. Which species tends to spend more time indolently amusing themselves rather than being focused efficiently on accomplishing the task at hand?

Sorry, but your Least Action "principle" isn't an example of a principle, it is a rather obvious example of someone confronted with an eminently reasonable objection resorting to making sh*t up.

Then there is #5 of your principles:

The simplest way to accomplish those effects would be to produce a primitive cell, endow it with a mechanism for evolving and diversifying into various life-forms, and then (at a few critical junctures) guide its evolution towards the desired targets.

Quite plainly the "simplest" way would be to design something that required no future intervention *at all*. But of course one could never be certain of this with an evolving, mutating system. In fact one could never be certain that intervention wouldn't be required frequently, or that one would achieve success even with frequent intervention. So your first and fifth principles contradict each other, as do your first and second (a mutating, evolving system necessarily removes the ability to limit one's future work), the first and third (inability to limit future work inconsistent with Least Action principle), the first anf fourth (whether such a system will give rise to intelligence is a crapshoot), etc., etc. Instead of all this self-contradictory Rube Goldberg rigmarole, let me show you the easy way:

- What's the easiest, most direct way for an intelligent entity to create sentient life?

- Reproduce.

You can thank me any time for resolving the probem in nine fewer steps than it took you.

I am more than willing to put $$$ on the claim that I understand evolution better than you.

This from the gent who declared, in a UD thread on whale phylogeny:

"You do realise that, with sex, all genetic trace can be lost in 2 generations, so it is impossible that these 'mistakes' [SINE inserts] can survive for millions of years to act as markers. Or are you too stupid to understand that?"

I don't believe in setting goalposts on Pluto. In a recent post, Professor Moran argues that our genome is full of junk DNA. See here: http://sandwalk.blogspot.com/2011/10/stephen-meyer-talks-about-junk-dna.html

My question is a simple one: how far back can we trace the flaws in our genome? If they go back to the very beginning of life, then that would be a problem for ID.

I think you are introducing confusing terminology. Is junk - functionless DNA - a 'flaw'? More generally, a 'flaw' would be a deleterious mutation - one which lowers the fitness of its bearers - ie reduces the number of offspring they can produce vs alternatives. Junk could be such a 'flaw', or it could not. It depends what it does to fitness, in the context in which it arises. If food is plentiful, junk need not be a punitive cost.

I doubt we could even agree on what constituted a 'flaw'. If there are redundant lines in my computer program, but they don't reduce its efficiency or effectiveness, they are hardly flaws, although they might interfere with maintainability. That last only matters if someone else needs to understand it.

As to tracing back to the beginning of Life ... this is goalpoasts-on-Pluto. The furthest back we can go is constrained by extant organisms we can examine, to determine their shared characteristics. We infer that these descend from LUCA. But LUCA was not the first cell, nor anything like. It was one of billions of cells alive in its time, themselves descended from a long lineage of cells with, it is almost certain, a non-DNA/protein system preceding the current transcription/translation setup.

So the short answer to your question is that we cannot trace those flaws back very far at all, because unless we know the selective milieu in operation, we cannot know what effect they would have upon an organism's fitness.

There is, however, absolutely no reason to suppose that 'flaws' are a recent 'invention'. Before DNA polymerase became good at error-correction, it is likely to have been sloppy. There is a trade-off between speed and fidelity. Is it 'flawed' to have a polymerase that corrects no errors but works very quickly? It creates flawed DNA. Or should we have one that takes a fortnight per chromosome but makes no mistakes? It creates 'perfect' copies but will be swamped by faster rivals.

Whether these are flaws or not is fundamentally adjudicated by ... Natural Selection. If there is an optimum, and a path to explore it, NS will tend to promote the DNA polymerase most fitting for the organism's circumstances. Those varieties eliminated by this optimisation are, arguably, 'flawed'. Benefit and detriment are relative, not absolute, terms.

You are making quite a remarkable claim, that DNA replication (and everything else about the organism) started out excellent and optimal, but - running completely counter to the selective gradient, since selection 'likes' optimality as much as any designer - has become worse, without compromising the Designer's goals.

Whether these are flaws or not is fundamentally adjudicated by ... Natural Selection.

I wonder if it might not be preferable to say *one* of the fundamental "adjudicators" is natural selection, because there are also at least contingency and drift, are there not? Contingency may select on a basis completely beside any genetic flaw (as the Chicxulub asteroid so effectively "selected" against many varieties of dinosaurs), and drift may allow flaws to pass if they are not terribly deleterious. (The random changeability over time in selective environments, and the fundamentally random aspects of contingency and drift, are at least some of the "crapshoot" factors inherent in evolution that make Vincent Torley's notion of a designer able to reach a designated resolution over billions of years with only the occasional nudge here and there such arrant nonsense.)

Hmmm. Maybe. Or maybe you are just too stupid to understand it. You don't understand how your point regarding the loss of alleles through sex demonstrates your howling inability to grasp some very basic concepts in evolutionary theory. Which in the context of your $$$ bet, is certainly worth a chuckle. I realise you won't be in on the joke.

I think that the role of meiosis in evolution might actually have occurred to someone at some point - and yet STILL they write papers on SINE markers. Why do you think that is? Are they too stupid to understand your Principle of Inevitable Allele Loss? Or might there be something in the bigger picture that you have missed?

"The Dunning–Kruger effect is a cognitive bias in which unskilled people make poor decisions and reach erroneous conclusions, but their incompetence denies them the metacognitive ability to recognize their mistakes. The unskilled therefore suffer from illusory superiority, rating their ability as above average, much higher than it actually is... "

Your so-called "scientific answer" has been effectively taken apart by others, and I'm wondering if you're going to respond to my comments and questions with something relevant and at least somewhat scientific?

I see that joe g is having his usual temper tantrum because he can't find any worthwhile answers to my comments and questions and the comments and questions from others.

Come on joe, try to convince me, with your vast scientific and evolutionary knowledge, that the many part, 'irreducibly complex' (at least and especially at the "core") island eco-system I described couldn't come about by stochastic processes/events/causes. Surely you can fit your designer/god in there somewhere?

Allan: Whether these are flaws or not is fundamentally adjudicated by ... Natural Selection.

Jud:I wonder if it might not be preferable to say *one* of the fundamental "adjudicators" is natural selection, because there are also at least contingency and drift, are there not?

Absolutely, but I think selective differential remains the only parameter that can be given the role of 'adjudicator'. The other processes are truly blind. We may look at bad design and sneer, but these may not be 'flaws' in any objective sense.

If the differential is zero, all is Drift, and selection has nothing to say upon what is or isn't a 'flaw' - its 'adjudication' is that it isn't. If there is a small selective differential, Drift may dominate, as selection's 'verdict' is too equivocal.

If the selective differential is strong, then we can start to see the less favoured allele as a 'flaw'.

Perhaps I am eccentric in seing selection as delivering a verdict by being silent! I see selection and drift as two parts of the same process - population resampling - with a diminishing role for Selection and greater role for Drift as the differential is turned down (despite having argued against this position in the past...). Nature isn't interested in what we see as flaws, and I'm not sure what objective standard we could apply other than that they have a 'sufficiently' detrimental effect on fitness to stand out as such.

Natural selection is just differential reproduction due to heritable (random) variation/ mutation. Meaning there isn't any selective gradient.

If there is a differential, then of course there is a gradient. Consider this version of your sentence: "A slope is just a differential in height above sea level between two points. Meaning that there isn't any gradient"

If Life were created perfect, it would tend to stay perfect - although of course Drift and environmental change could easily knock it off its current perch. In which case, it wasn't all that perfect, really. And what was the point of creating it so?

...I think selective differential remains the only parameter that can be given the role of 'adjudicator'. The other processes [drift, contingency]are truly blind.

Ah, got it, thanks. OK, just didn't want to lose sight of the fact that random processes can play a major role in which alleles make it to future generations and which don't. And of course some processes may be selective at one level (fitness for environment) and random/contingent at another (changes in the environment over time at a particular location).

Differential reproduction can occur for more reasons than heritable variation.

Absolutely. But where it is due to heritable variation, and there is a consistent relationship between variants (at a locus) and fitness, this sets up a selective gradient at that locus. The gradient may be zero - there is no difference between the alleles in their effect on fitness. Or it may favour one allele or the other. This will tend to push the population in the direction of the favoured allele, buffeted to a variable degree (depending on the steepness of the gradient) by Drift.

That would mean the gradientS are all over the place-

That is true. But in sexual species, at least, due to homologous recombination, each locus assorts in a quasi-independent manner, and each locus has its own local 'gradient' wrt alleles competing for that locus. That gradient (due to the differential in offspring numbers mediated by those alleles) tends to concentrate the fitter allele, if there is one.

But of course there are many loci, each with their own local gradient. Each locus is subject to the same tendency - the fact that 'the gradients are all over the place' (and, indeed, the slopes will change as circumstances do) does not preclude a tendency of the population to adapt, to multiple environmental factors simultaneously, and in multiple, complementary responses to the same environmental selective agent.

ya see there will also be competing advantageous traits.

Advantageous traits only compete if they are alleles at the same locus, or if there is antagonistic interference between the effects of different loci.

Unfortunely no one can test the premise that SINEs hung around intact enough for thousands/ millions of generations so they could be used as a genetic marker."

We have a pretty good handle on mutation rate, and on the approx. number of bases which form a potential target for degradative point mutations. If you crunch those numbers, you can get a pretty good idea how much degradation we can expect in neutral sequence.

I'll leave it to you to do that calculation, and demonstrate that the neutral sequence conservation we would expect over 50-odd million years is insufficient to allow detection of a particular pair of flanking sequences with and without the target SINE.

"Not that you will undersatnd that.

Strange that you want people to accept all this change is occurring yet alleged useless stuff will stay intact over thousands/ miliions of generations.

Truly pathetic."

You seem to be suggesting that both flank1/SINE/flank2 and flank1/flank2 must be functional, else they would have degraded beyond recognition over 50 million years. It is not clear why the SINE+ configuration would be functional in the whole of an apparent clade, while SINE- is functional in the whole of an apparent sister group - a pattern repeated hierarchically within the clades by use of other SINE markers. The organisms grouped by these markers are as diverse as deer, pigs and whales, so commonality of design seems a bit desperate.

It doesn't matter greatly for cladistics whether these markers are or aren't functional. But there is no conflict between them being nonfunctional and being sufficiently conserved to be detectable. Yes, change is occurring; yes, 'useless stuff' can stay (detectably) intact over millions of generations in the face of it.

"ID ... explicitly asserts that we puny humans can't say nothin' about the Designer, and explicitly denies that it (ID) has any interest whatsoever in attempting to learn anything about the Designer."

I've been defending ID for a few years now, so I think I know a little more about it than you. I suggest that you go and have a look at the definition of Intelligent Design on the Uncommon Descent FAQ Web page at http://www.uncommondescent.com/faq/#notsci:

"Intelligent Design is . . . a scientific investigation into how patterns exhibited by finite arrangements of matter can signify intelligence."

There's nothing in that definition that says human beings can't say anything about the Designer, or that ID theorists have no interest in learning about the Designer. That's your interpretation of what ID is baout; it's not mine.

You claim that my "goal-vs-motive schtick is a distinction without a difference." Nonsense. Two people may have the same goal - to become a multi-millionaire - but different motives. For instance, the first person's motive might be that she wants permanent financial security, while the second person's motive might be that he wants to prove to his father that he is not a failure.

You mentioned the plantaris tendon. Here's a reply by a creationist anatomist:

http://creation.com/plantaris-vestigial

I think I'll take his word over yours. And even if he were wrong, your remark fails to answer my original challenge: "If you can design a radically simpler cell than the ones we find in Nature, with the same biological functions and capacity to evolve, then please do." "Radically simpler" does not mean: missing just one part.

I really don't see what your problem is. The medieval theory that the planets influence our behavior could be called a scientific theory, like the phlogiston theory. Both theories turned out to be wrong. ID, like all good scientific theories, is falsifiable. Prove that a bacterial flagellum can be generated by simple physical processes that require no foresight, and you've falsified ID.

Thank you for your post. The Least Action principle can be formulated in a mathematically rigorous manner:

"Each way in which the Designer might accomplish His desired goals - i.e. the production of intelligent and sentient life-forms - can be viewed as a recipe, with a certain number of steps, where each step in a given recipe corresponds to a separate activity by the Designer. Now let's suppose that each step provides a complete description of an activity performed by the Designer in the most concise possible terminology. Thus each recipe is a complete but maximally concise description of a series of steps that would allow the Designer to get from the first living cell to His desired goals: intelligent and sentient life-forms, as well as whatever other life-forms are required to support them. There are many recipes, because there are many pathways to that goal. Some recipes are longer than others. According to the Least Action Principle, the Designer will select the shortest recipe."

Another thing I'd like to make clear is that I don't believe in true randomness. If the Designer is the Creator of the cosmos, then the only kind of randomness He could generate would be pseudo-randomness. Hence mutations are not truly random; they're simply unbiased, like the roll of a die. Ditto for quantum effects. We can't spot a pattern, but that doesn't mean there isn't one.

Thus when you argue that "a mutating, evolving system necessarily removes the ability to limit one's future work," you're simply mistaken. Until the arrival of beings possessing libertarian freedom (i.e. moral agents like us), the Designer could have predicted the evolution of the cosmos down to the finest detail. However, as anyone who's played billiards will realize, you'd need pinpoint accuracy to guarantee the production of a desired effect in the distant future. In other words, you'd need to specify your initial conditions to N decimal places, where N is very large.

Front-loading is one way of producing intelligent and sentient life-forms, but it requires an incredible degree of fine-tuning, making the description of the initial conditions very long. Separate creation of each species is another way, but because species share many of their genes, there's a lot of duplication in the descriptions - and yet, each species has to be specified separately, because it's created separately, so the total description is unnecessarily long. Creation of a single cell, followed by a specification of a sequence of mutations that will get you to each of your goals (i.e. each of the various intelligent and/or sentient life-forms we see today) in the shortest possible time (given what's happening on Earth in the meantime), avoids the need for duplication, as the life-forms branch off from each other. This way of generating intelligent and sentient life-forms will therefore have the shortest overall description. It's the shortest recipe, and therefore the one the Designer would pick. Intelligently guided evolution is the way to go.

"Why would it take four billion years?" you might ask. In a nutshell: terra-forming. That's what the Designer did to the early Earth. The earliest organisms were created in order to help transform the Earth into an environment hospitable to intelligent and sentient life-forms. That necessarily takes time. "But why not make the Earth hospitable from the start?" Because even if you did, it wouldn't stay that way. The Earth needs a complex system of natural cycles to keep its climate, geology and ecosystems stable. Inhospitable as it was, the primordial Earth was the best environment to set up those cycles in the first place. These cycles had to take root and build on each other, in a set geological sequence.

Thank you for your post. You write that the furthest back we can go in time is to the last universal common ancestor (LUCA). But according to Wikipedia, LUCA lived 3.5 to 3.8 billion years ago. The earliest life cannot have lived much earlier than that: probably it only goes back to 4 billion years ago.

I maintain that if we can go back to LUCA, we'll probably one day figure out what the very first living thing looked like.

When I said the first living thing was optimal, I was thinking of the genetic code. See this paper:

http://genome.cshlp.org/content/17/4/405.long

The authors cautiously describe the genetic code as nearly optimal. See also Freeland, S.J., Hurst, L.D.(1998) The genetic code is one in a million. J. Mol. Evol. 47:238–248.

What I'd predict is that the genetic code isn't just one in a million; it's the best code you could wish for, given the conditions that prevailed on the primordial Earth, and given that your goal is to engineer the evolution of intelligent and sentient life-forms. If anyone can show that evolution could have proceeded slightly better with some other code, that would count against the particular version of Intelligent Design I am proposing here.

You write that the furthest back we can go in time is to the last universal common ancestor (LUCA). But according to Wikipedia, LUCA lived 3.5 to 3.8 billion years ago.

I'd be unwilling to pin too hard a date on it. But there is a 'horizon' there that renders deeper probing pretty speculative.

The earliest life cannot have lived much earlier than that: probably it only goes back to 4 billion years ago.

True, but it's worth pointing out mind that even the 300 million year uncertainty between the quoted LUCA dates is a looooong time!

I maintain that if we can go back to LUCA, we'll probably one day figure out what the very first living thing looked like.

I think you're probably wrong on that. The DNA-RNA-protein system derived from LUCA is highly unlikely to date back to the earliest forms.

When I said the first living thing was optimal, I was thinking of the genetic code.

The criteria by which Freland & Hurst and others measure optimality relate to codon misread tolerance (the same or a chemically similar acid) and transition/transversion bias (misreading one purine or pyrimidine as the other is more frequent than reading a purine as a pyrimidine or vice versa). However, both of these properties can be derived neutrally, from expansion of a fewer-than-20-acid code with strong selection against disruptive substitutions. This code can only expand by codon reuse. The least disruptive codon reuses will be those that introduce chemically similar acids, with the result that future misreads will appear as if designed to have chemically similar 'neighbourhoods'. Transition/transversion bias protection, meanwhile, arises from the lack of triplet specificity in the aaRSs that mediate the code. The codon binding site in a fourfold degenerate assignment is blind to one base. To split this into two twofold degenerate sites requires only that purines and pyrimidines be distinguished from each other at that formerly 'blind' position. It does not need to distinguish all 3 positions specifically. Since there is a greater incidence of failure to distinguish purines from each other than from pyrimidines (transition-transversion bias), more misreads keep the same acid - again, an apparently designed feature falls out from the mechanics of the system. see here Note that the author was able to 'beat' the natural code a significant number of times with one model.

(Yes, I know someone designed the models :0). But they were built to explore constraints, not to optimise the resultant codes)

Vince arrogantly asserted (along with a lot of other ridiculous crap):

"I've been defending ID for a few years now, so I think I know a little more about it than you."

Well then, you should have NO problem with scientifically explaining every aspect of it in minute detail (including the actual design process), and with identifying the alleged designer, and with showing all the scientifically testable evidence that verifies ID and your identification of the alleged designer.

Oh, and why are you avoiding my points and questions about the island eco-system?

Another thing I'd like to make clear is that I don't believe in true randomness. If the Designer is the Creator of the cosmos, then the only kind of randomness He could generate would be pseudo-randomness. Hence mutations are not truly random; they're simply unbiased, like the roll of a die. Ditto for quantum effects. We can't spot a pattern, but that doesn't mean there isn't one.

Thus when you argue that "a mutating, evolving system necessarily removes the ability to limit one's future work," you're simply mistaken. Until the arrival of beings possessing libertarian freedom (i.e. moral agents like us), the Designer could have predicted the evolution of the cosmos down to the finest detail. However, as anyone who's played billiards will realize, you'd need pinpoint accuracy to guarantee the production of a desired effect in the distant future. In other words, you'd need to specify your initial conditions to N decimal places, where N is very large.

Sorry, but you are quite clearly and demonstrably incorrect. As you might imagine, the strangeness of some of the predictions of quantum physics over the past century or so has engendered thousands of quite sensitive experiments designed to test exactly the proposition you speak of - are things really fundamentally random, or are we just not seeing the pattern? (Yes, there are experiments that can test this precise question. The designs of many of them are tremendously clever.) The answer, verified in *every single case*, has been that yes, randomness is fundamental.

Moreover, randomness (uncertainty, if you prefer) is just one aspect of quantum physics; it is mathematically and as a matter of physical law interdependent with other aspects that have also been exhaustively tested (quantum physics has been called the best tested theory in the history of science) and shown to be true, all of which would have to be simply thrown out if what you say were actually the case.

For example, the problem that essentially started quantum theory 110 years ago is the "blackbody radiation problem." If classical physics is correct (your "billiard ball" concept), there is no way to limit blackbody radiation - it would be infinite. We know the laws of thermodynamics don't behave this way in real life. Quantum physics is the reason why.

Now of course there's a chance that you're smarter than Max Planck (the fellow who solved the blackbody radiation problem) or Werner Heisenberg (who formulated the uncertainty principle). If you can provide me a classical-physics solution to the blackbody radiation problem, that will go a long way toward convincing me you could be right. Of course if you can't, then all your talk about no true randomness is utterly worthless unscientific blather, isn't it?

(Oh, by the way, if you want to quote-mine Einstein about God not playing dice with the Universe, try looking up "Einstein-Podolsky-Rosen," a/k/a "EPR," some time. The EPR conceptual criticism of the uncertainty principle was experimentally tested and uncertainty was shown to be correct. Uncertainty in the EPR situation is in fact so fundamental that it paradoxically appears to facilitate faster-than-light communication, a situation called "quantum entanglement.")

The article points out that local hidden variable theories make predictions that are at odds with quantum mechanics. That's no skin off my nose, as the Creator of space-time is not confined to one location.

http://plato.stanford.edu/entries/qt-epr/#3.2

This article is even more cautious about what Bell's theorem shows.

"Bell's theorem is often characterized as showing that quantum theory is nonlocal. However, since several other assumptions are needed in any derivation of the Bell inequalities ..., one should be cautious about singling out locality as necessarily in conflict with the quantum theory.... Even though the Bell theorem does not rule out locality conclusively, it should certainly make one wary of assuming it."

Max Planck, you say? When he was asked by The Observer, "Do you think that consciousness can be explained in terms of matter?", Max Planck replied:

"No, I regard consciousness as fundamental. I regard matter as derivative from consciousness. We cannot get behind consciousness. Everything that we talk about, everything that we regard as existing, postulates consciousness."(Planck, as cited in de Purucker, Gottfried. 1940. The Esoteric Tradition. California: Theosophical University Press, ch. 13).

I'd like to apologize for not getting back to you earlier. This thread is getting rather long, and I somehow missed your reply. Re your proposed core of the island eco-system (1. the fresh water, plus 2. the island itself): I'm afraid your proposed core is too small. It doesn't have a function. By themselves, water and an island do nothing. You need living things. But if you add living things, the problem is that no particular species is absolutely essential to the functioning of the eco-system, except for the last one you happen to remove (by definition, if it is taken away, the eco-system ceases to be).

However, let's suppose that one particular species (e.g. some alga, or perhaps some plant), is indeed essential to island eco-systems. You've still only got three parts - island, water and organism - so you might just as well say that a plant growing alone in the soil is an irreducibly complex system.

There's another reason why the system described above isn't irreducibly complex: the parts are not "well-matched", as required by Michael Behe's 1996 definition: "By irreducibly complex I mean a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. (Behe, "Darwin's Black Box," 1996, p. 39). The sea and the island are hardly "well-matched." They don't fit together like hand and glove. Configuration is unimportant. Ditto for the living thing and the island it inhabits.

Do I think an island eco-system would need to be intelligently designed? No. First, the argument only works for multi-part systems. Three is hardly "multi." Second, the parts aren't well-matched. Finally, the eco-system is a bad parallel to Behe's flagellum case: in the latter case, all the components were parts of a living thing, which made it difficult to envisage how that system could have evolved naturally, and therefore made intelligent design a plausible explanation. In the case of the three-part eco-system, two of the parts - the island and the water - aren't even parts of something alive. They're just there at the beginning, so that means only one part (the essential species) has to appear on the scene, after being carried there by sea.

Re Collins' article: Collins does not argue that "humans are the pinnacle of special creation," since the key fact he invokes theism in order to explain is "the existence of a material spatiotemporal reality that can support embodied moral agents." He doesn't say "human beings," and he doesn't say we are alone in the cosmos. If you think theism is a bad explanation for fine-tuning, then my question for you is the one Huxley used to pose to his critics: "What is your alternative?"

I am sorry to bring these news to you, but quoting physicists on their opinions about souls and consciousness does not help anybody. When we talk about their discoveries in physics there is something beyond the scientists we hold to. That's their results, be it equations solved, experiments performed,long et cetera. When it comes to such esoteric shit so far out of their experimental and mathematical work, all I can say is that whatever they thought about such stuff is bullshit. That if we were able to discard the possibility that they were just quote-mined. In neither case (they really said it, versus they were quote-mined), the quotes are useless.

Actually, look deeper than that and notice that everything IDiots do is quote. They seem to be unable to actually look at data even when they quote something said by some scientist in an article.

As for this piece of yours:

Prove that a bacterial flagellum can be generated by simple physical processes that require no foresight, and you've falsified ID.

Actually no. Prove that there could have been a designer when the flagellum first came to be, show me the tools, the processes, the methods, everything that comes with a designer, and I might start to consider ID. It is not enough to convince yourself that nature alone would not do. You have to show how and what would do.

As of me. I have seen some pretty amazing stuff done by random mutation, selection, reproduction, recombination. Both by experiment and in computer simulations. Even designs made by such processes. I have also seen lots of evidence for the evolution of quite a lot of systems and biological "machines." Thus, I have no problem being convinced that flagella are the products of evolution. Results Vincent. That's what counts. A few random results here and there, well, I could doubt evolution by "just" natural processes. But the way things are today, doubting this is both ignorance and mere god-of-the-gaps fallacy.

If you think theism is a bad explanation for fine-tuning, then my question for you is the one Huxley used to pose to his critics: "What is your alternative?

I would have a few observations:

Fine-tuning? First demonstrate such a thing is there, and what such fine-tuning is for. Because if you start with us, then the universe, it does not seem as if the whole universe is filled by us. Not even the whole solar system is filled by us. Thus, if there is fine-tuning, it is not for us. For what is this fine-tuned then?

If you are going to claim that our planet is fine-tuned for us, then, again, there is plenty of places where we can't survive. Maybe it is fine-tuned for microbes instead.

Theism is a bad explanations for anything. First show that gods are there, then we talk about theism explaining something. As of me, if it failed to explain thunder, volcanoes, long et cetera, I don't expect it to explain anything. Imaginary beings are not explanations, but wishful thinking.

Alternative? Again, first show that there is such a thing and start with what this this fine-tuning would be for.

Other than that, why this universe is the way it is? Well, because it is the way it is. That's why.

"Re your proposed core of the island eco-system (1. the fresh water, plus 2. the island itself): I'm afraid your proposed core is too small. It doesn't have a function. By themselves, water and an island do nothing.

You need living things. But if you add living things, the problem is that no particular species is absolutely essential to the functioning of the eco-system, except for the last one you happen to remove (by definition, if it is taken away, the eco-system ceases to be)."

----------------------

First of all, I have to say that I was hoping for a better argument from you, and a more honest one. It is very frustrating trying to deal with someone who is so determined to not face facts and to re-define words to suit their extremely biased agenda. For instance, "multi" means more than one, and three is more than one.

And your lack of knowledge about nature is obvious. I kept things simple thinking that you might be able to envision what would be involved in an island eco-system, at least when pertaining to the ID argument about IC. You try to sound as though you see the vast complexity in nature but when your assertions and beliefs are challenged you sound as though you can't see past the end of your nose. I have many things in mind to refute your ignorant assertions and I could type them all out but it would essentially turn out to be a very lengthy lesson in biology, geology, meteorology, and a lot of other '...ologys', and I don't have the time or patience for that. So, I'll just point out some things, and suggest that you get a clue.

Now, I proposed the removal of the land or the fresh water as examples of the 'irreducible core' of the eco-system, but I didn't say that they're the only examples.

I can't imagine how you can think and say that neither of them have a "function". Without fresh water and/or land there wouldn't be an island eco-system.

You ID pushers love to argue that every teeny tiny part of something has to be there for the entire thing to be 'functional', but somehow you also think that an island eco-system can and will function without an island.

You also love to argue that every teeny tiny part of something (e.g. a "system") is critical as to determining whether it could evolve by natural, stochastic processes/causes/events, but ignoring or removing the island from an island eco-system isn't important to you. I would think that you would be the one arguing that the land or fresh water, for example, are absolutely critical parts of the "core" of the island eco-system! Of course you would be arguing that IF you thought you could get away with crediting your chosen designer/creator god with designing and creating the land and fresh water of the island eco-system.

Since you think that land and fresh water don't have a function, maybe you could tell me what this island Earth would be like if there were no land and/or fresh water? Do you still want to say that land and fresh water have no function?

And why don't you want to give your chosen designer/creator god credit for designing and creating the atoms that land and fresh water are made of? I thought "God" is alleged to have designed and created, well, everything.

I see that you're relying on the presence of a single species in your description of an eco-system. That's very odd coming from someone who says that an island eco-system has to have "multi" parts to be an eco-system and that the only parts that are required for it to be an eco-system are the biological ones. It's also odd coming from someone who would argue that the more parts there are the more a system (and "complex") it is. And maybe the most odd thing of all is that you're ignoring (or deliberately and conveniently excluding?) the other abiotic parts of the island eco-system in your "three-part" claim.

And I hope you don't think that an island "eco-system" would have only one species (for long anyway)?

You said:

"By themselves, water and an island do nothing. You need living things."

Yeah, an "eco-system" needs living things, and for the sake of discussion I'm content with "living things" as meaning two or more species.

For your perusal:

http://en.wikipedia.org/wiki/Ecosystem

http://en.wikipedia.org/wiki/Trophic_level

http://en.wikipedia.org/wiki/Abiotic

You might notice that there's more to an eco-system than just the "living things", such as land (bedrock, soil, etc.), water (fresh or otherwise), atmospheric gases, temperature, sunlight, chemicals, etc. They're all 'parts' of the system and they certainly are "multi". You should also notice that the abiotic parts are critical to the existence and function of the system, and it could be easily argued that any one of the "core" abiotic parts is more critical than any one of the biotic parts or even most of the biotic parts put together, in regard to an 'irreducibly complex core'. For example, without an island (land, an abiotic part), there would be no island eco-system at all, no matter how many "multi", biotic parts there are.

You also seem to be unaware of the fact that living things contain and depend on internal water, which of course is obtained from external sources. Do you also think that internal water has no function?

And speaking of 'internal', you apparently think that "living things" are not affected by, dependent on, or connected to the 'external' environment. Can you point out any 'living thing' or any part of any 'living thing' that is absolutely impervious to and not dependent on its environment?

Wow. And I do mean WOW. They are CERTAINLY parts of the system and they are absolutely necessary for the system to 'function'.

You also said:

"...no particular species is absolutely essential to the functioning of the eco-system, except for the last one you happen to remove..."

So, you're saying that just one species is needed for it to be a functioning eco-system, yet you say that the two other parts I mentioned (land and fresh water) are irrelevant to the functioning of the eco-system and that three parts is too small and, well, what the fuck are you saying??

Besides, the effect of the removal of any species is very debatable, especially when considering a well established eco-system, and when considering the keystone species. Since we're talking about IC, it should be kept in mind that partial or complete removal of any species, and especially keystone species, can or will affect the 'function' of the system and could cause catastrophic effects to the "core" or otherwise. And of course, that's just the biotic part of the system.

I think that your "aren't well-matched" argument is lame. A healthy, long term eco-system is "well-matched" and it could be said that even a new island is a good match for some living things. If it weren't a good match no living thing would ever survive or thrive on the island and no long term island eco-system would come about. And no, that doesn't mean that the new island is fine tuned. It just means that some species are able to survive on a new island (e.g. some autotrophs, and birds that can nest on it but feed from the surrounding sea).

'Well-matched' is also a matter of opinion and there are many things (parts) within living things and in natural eco-systems that don't appear (to humans) to be "well-matched". Should your chosen designer/creator god get credit for those things too, or is credit reserved only for the things that ID pushers describe as "well matched"?

Is the mammalian recurrent laryngeal nerve "well-matched"? Is it 'configured' well? It works, doesn't it?

Are you sure you want to say that? I thought it was you IDiots who say that configuration is extremely important?

Proper, suitable, necessary, perfect, lousy (take your pick) "configuration" in nature is also a matter of opinion from our human point of view, and nature does a good job at coming to a 'working' configuration. Working meaning that it works for some living things (or parts of living things) and not for others. Nature doesn't care whether everything works or whether everything survives and it isn't 'fine tuned' for a particular goal (like producing embodied moral agents). What works survives and reproduces. What doesn't work or reproduce is gone. Morality has nothing to do with it. If fine tuning were real, nothing would ever die or go extinct, and every living thing could easily live anywhere and everywhere.

You said:

"...he (Collins) invokes theism in order to explain is "the existence of a material spatiotemporal reality that can support embodied moral agents." He doesn't say "human beings," and he doesn't say we are alone in the cosmos. If you think theism is a bad explanation for fine-tuning, then my question for you is the one Huxley used to pose to his critics: "What is your alternative?"

You've got to be joking. You know damn well that Collins is referring to humans and that you think that way too. You godbots obviously believe that humans are the pinnacle of your chosen god's creations. By the way, have you ever considered the fact that the Earth and the non-human life on it would get along just fine without humans but life on Earth (including humans) would have a REAL HARD time (to put it mildly) getting along without bacteria? Hmm, maybe bacteria is the pinnacle of your chosen god's creations. LOL

My alternative? Well, I would say that living things adapt to the their environment and that the ones that don't adapt are eliminated. The "fine-tuning" crap is absurd.

Think about this:

Is the new island I mentioned fine tuned for whatever living things happen to get there or do the living things that happen to get there have to adapt to the island in order to survive? And later on, after many living things reside on the island, is that many part eco-system then fine tuned for whatever other living things happen to get there or do those new arrivals (and the ones already there) have to adapt in order to survive?

If you happened to get to that island, and all you had is the shirt on your back, do you think that the island would be fine tuned for you or would you have to adapt to the island (including all the parts of the eco-system) in order to survive?

That's all I can stand to type right now. My patience, what there was of it, has run out.

Ah. Well since you were around prior to the last shower, perhaps you had time to read all the way to the end of the article?

In August 2011, Roger Colbeck and Renato Renner published a proof that any extension of quantum mechanical theory, whether using hidden variables or otherwise, cannot provide a more accurate description of outcomes, assuming that observers have free will.

"Observers" and "free will" have special meanings in that sentence, shown by the quote from the journal article in the footnote:

"In the present work, we have ... excluded the possibility that any extension of quantum theory (not necessarily in the form of local hidden variables) can help predict the outcomes of any measurement on any quantum state. In this sense, we show the following: under the assumption that measurement settings can be chosen freely, quantum theory really is complete."

So observers are those who measure, and free will is the ability to make an honest measurement. Under those circumstances, regardless of which interpretation/extension of quantum theory you choose, there is no ability to improve predictions of future outcomes - no "clockwork [or in your case billiard ball] universe." Thus the close predictive ability on which your picture of a Creator's method depends doesn't exist according to the best-confirmed scientific theory of the current era. (If such predictive ability did exist, it would completely obviate the need for the "tweaking" that is also part of your picture, which as I pointed out a few comments ago is only one of several self-contradictions in your model.)

Thank you for helping to show that the model of ID and the creation of irreducibly complex systems you espouse contradicts quantum physics, to say nothing of modern evolutionary biology.

Behe: "If natural selection were shown to be capable of producing a system of a certain degree of complexity, then the assumption would be that it could produce any other system of an equal or lesser degree of complexity."

joe g: "Pathetic- If you don’t like the design inference just start producing evidence that stochastic processes can design irreducibly complex configurations."

joe g: "Two parts can count as IC- one part can."

joe g: "The argument from IC involves our knowledge of cause and effect relationships. That is every time we have observed IC (or CSI) and knew the cause it has ALWAYS been via agency involvement- always, 100% of teh time.

Therefor when we observe IC (or CSI) and did not directly observe it arising we can safely infer agency involvement was required.

That is until someone comes along and demostrates that stochastic processes can produce it. Then Newton’s First Rule applies and the design inference is refuted."

joe g: "Tell you what dmullenix, to refute the design inference all YOU have to do is actually step up and produce positive evidence for YOUR position. Then Newton’s First Rule applies and ID is refuted."

----------------Newton’s first rule: We ought to admit no more causes of natural phenomena than such as are both true and sufficient to explain their appearance.-----------------

vjtorley: "A functional system is irreducibly complex if it contains a multipart subsystem (i.e., a set of two or more interrelated parts) that cannot be simplified without destroying the system’s basic function. I refer to this multipart subsystem as the system’s irreducible core."

vjtorley: "Recall the definition of irreducible complexity: “a set of two or more interrelated parts that cannot be simplified without destroying the system’s basic function.”"

vjtorley: "Do I think an island eco-system would need to be intelligently designed? No."

Behe: "By irreducibly complex I mean a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. (Behe 1996, 39)"

Dembski: "A functional system is irreducibly complex if it contains a multipart subsystem (i.e., a set of two or more interrelated parts) that cannot be simplified without destroying the system’s basic function."

gpuccio: "The argument from IC applies specifically to all non intelligently designed systems."

gpuccio: "I have a lot of examples of systems that are not designed: the configuration of sand in a beach, the form of mountains, weather, the signals from a pulsar, radioactive decay, and so on."

The island eco-system I've described easily meets the definition of a multi-part system, even when describing it only basically, and it should be apparent to anyone that such a system would become more complex (at least biologically) as time goes on from its first appearance above the surface of the sea (unless it were destroyed or made lifeless by further volcanic actions).

Every living thing that resides on the island would not be there if it weren't for the island itself, and if other 'core parts' were removed, like weather, atmospheric gases, fresh or other water, sunlight, etc., there would be no eco-system. Even gravity is necessary for the eco-system system to 'function'.

Idiots love to say that the analogies non-IDiots use are irrelevant or not biological or whatever, but if you look at the analogies IDiots use to support their IC and ID assertions, like machines, computers, airplanes, engines/motors, wiring diagrams, and a ton of other irrelevant, man-made stuff, they have no room to complain about analogies non-IDiots use.

An island eco-system is biological (biotic), geological, and meteorological, and a long list of other more specific '...ologicals' or similar terms could be legitimately applied.

When it comes to 'parts', and whether they interact, are interrelated, complex, configured, irreducible, etc., the island eco-system could be described and analyzed at many scales, including right down to atoms and their parts.

The island eco-system would come about by non-designed processes/causes/events. It would have sub-systems or whatever other basic requirements IDiots say are necessary to be a complex system with an irreducible core, and depending on the scale at which the eco-system is looked at, it could be described as having 'multi' (or many) cores that could be described as irreducible when it comes to 'function'.

Hey joe g and vjtorley and the rest of you IDiots: designed IC, and ID, are hereby refuted. :)

Oh, and keep in mind that this entire planet is an island and it's a system within a system within other systems, and it (Earth) has sub-systems galore and many irreducible 'cores'.

If you think you have a good argument against my points, let's see it.

Thank you for your post. You really do need to be a bit more critical when reading quantum physics papers. If a researcher claims to have proved something, it's best to with-hold judgment until other scientists have had time to critically evaluate it. I haven't seen anyone making waves about this paper. That's why I didn't cite it. Look at the date: August 2011.

But let's suppose the authors are right. What Colbert and Renner they claim to show? "we have ... excluded the possibility that any extension of quantum theory ... can help predict the outcomes of any measurement on any quantum state." Can help whom? Observers like ourselves, who are inside space-time. What about beings in a universe outside our own? What about beings outside space and time altogether? We don't know, and if you believe that Colbeck and Renner have proved that even these beings can't possibly know about quantum states in any other way than the way we do, then you're more gullible than I thought. But hey, why don't you ask them? TheCreator is not bound by the laws that apply to creatures, unless we're talking about the laws of logic.

The Whole Truth

Thank you for your post. If you're going to cite definitions of irreducible complexity, kindly cite reputable authorities. I'm not one. Nor is Joe G. Dembski is. Behe is. Also, if you're going to cite people, it pays to interpret their writings charitably. It's easy to tear down an argument by citing an isolated passage from someone you want to discredit; lawyers do that all the time. It's much harder to try and present your opponent's case in the best possible light and then refute it. I've already explained that I don't like your island eco-system example because the land and sea don't inter-lock closely enough with the organisms. The fact that the parts have functions isn't enough; they have to inter-connect. And I'm aware that there are many species on an island eco-system, but you can't nominate one that would be essential.

However, Guillermo Gonzalez has written a book called The Privileged Planet in which he argues that several natural cycles that occur on Earth are in fact the product of intelligent design. I like these examples better, because the components can indeed be said to be "well-matched." Plate tectonics is one example they talk about at length in their book. So I'm quite happy to agree that many of the Earth's sub-systems are designed.

By the way, I do believe the Designer conserves everything in being.

You write that you could teach me "lengthy lesson in biology, geology, meteorology..." What are your scientific qualifications? Can you define a phylum, and can you tell me which one has the most species? Can you recite the geological timetable backwards, as I can (dates and all)? Can you offer an educated opinion on Dr. Roy Spencer's views on global warming? Just asking.

Negative Entropy

For an answer to your questions about why most of the universe is hostile to life, please see my post at http://www.uncommondescent.com/intelligent-design/the-universe-is-too-big-too-old-and-too-cruel-three-silly-objections-to-cosmological-fine-tuning-part-two/

You write: "show me the tools, the processes, the methods, everything that comes with a designer, and I might start to consider ID." My answer is Arthur C. Clarke's third law: "Any sufficiently advanced technology is indistinguishable from magic." If you found a 1 x 4 x 9 monolith on a faraway planet you'd say it was designed, and never mind the tools or processes. The designer's M.O. is always the last thing you find out - you'd need to be nearly as smart as the designer to grasp that.

The Creator is not bound by the laws that apply to creatures, unless we're talking about the laws of logic.

Oh, and here I thought we were discussing science. If you are talking about supernatural phenomena, then of course laws pertaining to natural phenomena, e.g., quantum mechanics, do not currently take supernatural intervention into account, as no observation has ever indicated the slightest need to do so. (Don't know why supernatural beings/phenomena should be restricted by logic, either, but hey, it's your vision of a supernatural Creator, so I won't disputandum your gustibus.)

There would be an overwhelmingly high requirement for evidence of the existence of such a being or beings, if one wishes to overthrow all existing science in Its/His/Their name(s). So far, no evidence at all exists, let alone the overwhelming amount required. When and if it does, I will of course be ready to change my view that science has proved pretty good at explaining things so far.

Vincent, I have to admit that when I read your response I laughed until tears ran down my cheeks.

I did quote Behe and Dembski, and ALL of you ID pushers speak as though you're the only "reputable authorities" on anything and everything. That's one of your biggest flaws. You're a bunch of egotistical and narcissistic authoritarians who think that everyone else should swallow and obey your every word without question.

You said:

"Also, if you're going to cite people, it pays to interpret their writings charitably. It's easy to tear down an argument by citing an isolated passage from someone you want to discredit; lawyers do that all the time. It's much harder to try and present your opponent's case in the best possible light and then refute it."

That is absolutely hilarious coming from you. Charitably? Don't you mean that I and others should just take your word for everything?

I'm as charitable as I possibly can be but being charitable isn't what matters, especially when your arguments (and those of your fellows) are based on non-evidential, non-scientific religious fairy tales, and a dishonest religious and political agenda that is trying to ruin or replace science.

And where's your charity and "best possible light" when it comes to the ToE, and my example of the stochastic island eco-system? When it comes to trying to "tear down an argument by citing an isolated passage from someone you want to discredit" you ID pushers are unsurpassed. You really should have a talk with kairosfocus, joe g, bornagain77, uprightbiped, barry arrington, o'leary, luskin, and all the rest of the IDiots about quote mining and misrepresenting what scientists say.

You "don't like" my example? This may come as a shock to you but what you like or "don't like" is irrelevant. My island eco-system example crushes your design is required IC assertions. And many other people have crushed the IC and ID assertions over and over too.

You also said:

"The fact that the parts have functions isn't enough; they have to inter-connect."

Ah, first it was that the island itself and the fresh water have no function, but now it's "the land and sea don't inter-lock closely enough with the organisms" and that they don't "inter-connect". Can you say 'moving the goalposts'? And the other IDiots say "interacting" or "interrelated".

Besides, all the parts interconnect, interrelate, and/or interact closely. You apparently think that those terms mean that absolutely everything must be successful and survive and thrive in order to meet your definition of those terms.

If you were completely engulfed in fire, you and the fire would be interconnected, interrelated, and interacting, but I doubt that you'd survive and thrive. There would be a lot of other things interrelating, interconnecting, and interacting in that fire too.

And anyone with a clue knows that any organism that does survive and thrive in the island eco-system would have to interconnect, interrelate, and/or interact (take your pick) in a successful and adaptive way. Otherwise they wouldn't survive and thrive. No matter how many words I read that are spewed by you ID pushers, I am still amazed at how ridiculous your arguments can be.

Of course you like The Privileged Planet. It supports your belief that the Earth is specially created and so are you!

So, you're "quite happy to agree (with Gonzalez) that many of the Earth's sub-systems are designed" when it comes to plate tectonics, but you already said that you don't believe that the island eco-system I used as an example would be designed. Obviously you aren't aware of the fact that volcanic islands are produced by interaction, interrelatedness, and interconnectedness with plate tectonics (to use the words you IDiots use). Oh, and the island itself is just one part, but an essential part, of the "core".

You asked:

"What are your scientific qualifications?"

My scientific qualifications are not important for the purposes of this debate. Unlike you IDiots, I don't feel the need to bring my qualifications as some sort of an 'authority' into a debate. I'll let my words speak for me.

You said:

"You write that you could teach me "lengthy lesson in biology, geology, meteorology..."

I didn't actually say that. I said it would turn out to be a lesson, etc., etc., but now that you mention it I could try to teach you but I doubt that it would stick. Your mind is obviously made up about your chosen designer/creator god.

You said:

"You write: "show me the tools, the processes, the methods, everything that comes with a designer, and I might start to consider ID.""

I don't recall saying those words in quotes. I'll gladly admit that I did if you show where I said them. And whether I said them or not they're not an unreasonable request. If you're so concerned with what is "scientific" you should realize that it takes more than your religious beliefs to present a scientific argument/inference/hypothesis.

The rest of what you wrote isn't worth responding to. You're obviously just looking for anything that you think will support your beliefs.

Ya know, Vincent, I can't help but think that you have doubts about your religious beliefs. Otherwise, why would you care about what science does or says? In some ways you seem like a sharp guy and a nice guy but you're hindered by the ball and chain of religious dogma. Just think what you could accomplish if you cut off that ball and chain. It's not too late.

I think I am just intervening in the conversation you were having with both TWT, and Jud, both of whom have given you penty of good answers that you happily misread or read only halfway, as I think you read my comments.

So, I will try to answer what you told me and not add to anything you are exchanging with others to avoid confusion.

Your link goes to something about "silly atheistic arguments against fine-tuning.=," which does not answer what I asked. It seems to me that you assume that I got those objections from somebody, while what I did is give you my two cents. Anyway, what's wrong with your linked answers:

1. The objections by atheists were not silly unless your answers were obvious. They are not obvious, thus the "atheistic" objections are not silly. It is quite reasonable to doubt that anything is fine-tuned ("for life" I assume as that's what your link mentions) if a lot of it does not have what it is supposed to be fine-tuned for.

2. My objections were not those, my point was that there is nothing demonstrating such fine-tuning, that from whichever point you look at it, it does not look fine-tuned for life (mostly no life around), nor for us (where there's life, it seems like the planet would be "fine-tuned" for microbes). SInce you linked to "atheistic" objections, I take that you prefer the planet to be fine-tuned for us, which it is obviously not.

3. Your non-obvious answers are non-answers. All you say for those two atheistic objections summarizes as: "the universe is this big and this old because that's the way it works." That does not need a god anywhere, let alone an omni-anything god (remember it is you who used the word "atheist," don';t blame me for adding a god to the soup).

4. To clarify the above:

a) The universe is big because otherwise there would be no way of making the building blocks for life. Well, for one this is wrong. Enough material for us would be available with our galaxy alone (probably with much less). For another, we must have a very different definition for fine-tuning, because it would seem like you assume fine-tuning out of a universe that, in order to have us, has to go through a lot for this tiny result. That does not look as if the universe is fine-tuned for life, but, again, as if we are just one little possibility among the many other things that could happen.

b) the universe is old because this age is required for it to be this big and have us here. Well, this translates into: because of the properties of the universe, it had to be this old in order for us to be here. Which means we come after, not as a forethought, but after what the universe is, we are the ones who are "fine-tuned" to what the universe is, not the universe so that we would be here. Thus, we might as well save the idea of a god and start with the universe. Is this clear?

Your problem my friend, is that you hold to rhetoric, rather than to reason.

The second thing, Arhur C clarke forgot this other principle: any sufficiently misunderstood natural process is undistinguishable from magic. We have lots of examples. For one, when volcanoes were misunderstood, they were gods themselves at times, god-produced at other times. That did not work that well, did it?

So I insist, show me the evidence for this designer's presence first. Assuming the designer to begin with is, well, silly. You assume a designer fine-tuned the universe, well, that leaves you with no way of proving that there is a designer. Why? because you can't prove that the universe required a designer from the way it works. Then, from our understanding of how it works it is easy to conclude that we are the products of this universe as it is and as it works. Thus, no need for a designer. That designer is something you put on top for no other reason than your religious beliefs (which I guess to be old-earth creationism, who knows if linked to Christianity or not).

A distortion of the Design argument which is based on the primacy of Reason in any cogent interpretation of reality. To reduce it to natural processes is self-destructive. Complex thought does not entail a multitude of thinkers! One is quite enough and satisfies the principle of parsimony incomparably more than millions of molecules...

Ecosystems are composed of a variety of abiotic and biotic components that function in an interrelated way.[39]The structure and composition is determined by various environmental factors that are interrelated. Variations of these factors will initiate dynamic modifications to the ecosystem. Some of the more important components are: soil, atmosphere, radiation from the sun, water, and living organisms.

Central to the ecosystem concept is the idea that living organisms interact with every other element in their local environment.

Eugene Odum, a founder of ecology, stated: "Any unit that includes all of the organisms (ie: the "community") in a given area interacting with the physical environment so that a flow of energy leads to clearly defined trophic structure, biotic diversity, and material cycles (i.e.: exchange of materials between living and nonliving parts) within the system is an ecosystem."[40] Within the ecosystem, species are connected and dependent upon one another in the food chain, and exchange energy and matter between themselves as well as with their environment.[41]

The human ecosystem concept is grounded in the deconstruction of the human/nature dichotomyand the premise that all species are ecologically integrated with eachother, as well as with the abiotic constituents of their biotope.

A smaller unit of size is called a microecosystem. For example, a microsystem can be a stone and all the life under it. A macroecosystem might involve a whole ecoregion, with its drainage basin.[42]

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.